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- PDB-6mft: Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in ... -

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Entry
Database: PDB / ID: 6mft
TitleCrystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain
Components
  • Gp120Envelope glycoprotein GP120
  • Heavy Chain glVRC01
  • Light chain glVRC01
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / glycans / germline / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell endosome membrane / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.315 Å
AuthorsWeidle, C. / Pancera, M. / Stamatatos, L. / Gray, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI081625 United States
CitationJournal: Elife / Year: 2018
Title: Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.
Authors: Andrew J Borst / Connor E Weidle / Matthew D Gray / Brandon Frenz / Joost Snijder / M Gordon Joyce / Ivelin S Georgiev / Guillaume Be Stewart-Jones / Peter D Kwong / Andrew T McGuire / Frank ...Authors: Andrew J Borst / Connor E Weidle / Matthew D Gray / Brandon Frenz / Joost Snijder / M Gordon Joyce / Ivelin S Georgiev / Guillaume Be Stewart-Jones / Peter D Kwong / Andrew T McGuire / Frank DiMaio / Leonidas Stamatatos / Marie Pancera / David Veesler /
Abstract: VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding ...VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy Chain glVRC01
L: Light chain glVRC01
A: Heavy Chain glVRC01
B: Light chain glVRC01
G: Gp120
C: Gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,02227
Polymers173,8926
Non-polymers6,13121
Water5,855325
1
H: Heavy Chain glVRC01
L: Light chain glVRC01
G: Gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,52214
Polymers86,9463
Non-polymers3,57611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint43 kcal/mol
Surface area34890 Å2
MethodPISA
2
A: Heavy Chain glVRC01
B: Light chain glVRC01
C: Gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,50013
Polymers86,9463
Non-polymers2,55410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint19 kcal/mol
Surface area34340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.082, 109.003, 103.225
Angle α, β, γ (deg.)90.00, 114.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-663-

HOH

21G-716-

HOH

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Components

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Protein , 1 types, 2 molecules GC

#3: Protein Gp120 / Envelope glycoprotein GP120


Mass: 38591.953 Da / Num. of mol.: 2 / Fragment: 426c core, residues 44-494 / Mutation: G459C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: M4Q8P8*PLUS

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Heavy Chain glVRC01


Mass: 25334.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain glVRC01


Mass: 23019.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 4 types, 17 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 329 molecules

#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.09M MgCl2, 0.09M Na Citrate pH 5.0, 13.5% PEG 4K, 0.1M LiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.315→50 Å / Num. obs: 83087 / % possible obs: 95.6 % / Redundancy: 7.4 % / Net I/σ(I): 23.4
Reflection shellResolution: 2.315→2.36 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.315→49.152 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 4260 5.13 %
Rwork0.2438 --
obs0.2464 83037 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.315→49.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12114 0 28 325 12467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312459
X-RAY DIFFRACTIONf_angle_d0.58816986
X-RAY DIFFRACTIONf_dihedral_angle_d12.4017489
X-RAY DIFFRACTIONf_chiral_restr0.0451968
X-RAY DIFFRACTIONf_plane_restr0.0032145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3151-2.34140.51681070.45571954X-RAY DIFFRACTION72
2.3414-2.3690.45221180.42592218X-RAY DIFFRACTION82
2.369-2.39790.50551490.40482365X-RAY DIFFRACTION86
2.3979-2.42820.42381310.38882357X-RAY DIFFRACTION88
2.4282-2.46020.38161360.38172498X-RAY DIFFRACTION91
2.4602-2.49390.44411350.37682492X-RAY DIFFRACTION92
2.4939-2.52950.39431470.35642547X-RAY DIFFRACTION94
2.5295-2.56730.42731520.35572635X-RAY DIFFRACTION97
2.5673-2.60740.41141640.32922646X-RAY DIFFRACTION98
2.6074-2.65010.38311300.31242753X-RAY DIFFRACTION98
2.6501-2.69580.39411560.32082627X-RAY DIFFRACTION98
2.6958-2.74480.38581680.30952683X-RAY DIFFRACTION99
2.7448-2.79760.38551250.30972692X-RAY DIFFRACTION99
2.7976-2.85470.40421530.32172678X-RAY DIFFRACTION99
2.8547-2.91680.38421480.3272691X-RAY DIFFRACTION99
2.9168-2.98460.37191450.28592717X-RAY DIFFRACTION99
2.9846-3.05930.34051340.27522716X-RAY DIFFRACTION99
3.0593-3.1420.31241220.2842709X-RAY DIFFRACTION99
3.142-3.23440.30561530.27192702X-RAY DIFFRACTION99
3.2344-3.33880.31781640.26612696X-RAY DIFFRACTION99
3.3388-3.45810.31571310.24752712X-RAY DIFFRACTION99
3.4581-3.59650.28651430.24312716X-RAY DIFFRACTION99
3.5965-3.76010.27691500.23312730X-RAY DIFFRACTION99
3.7601-3.95830.3281310.20732738X-RAY DIFFRACTION99
3.9583-4.20620.231450.19782714X-RAY DIFFRACTION99
4.2062-4.53070.23551460.18422743X-RAY DIFFRACTION100
4.5307-4.98620.20521610.18412712X-RAY DIFFRACTION100
4.9862-5.70680.2341380.19482760X-RAY DIFFRACTION100
5.7068-7.18640.26631460.22512778X-RAY DIFFRACTION100
7.1864-49.16350.23511320.20042798X-RAY DIFFRACTION98

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